Dear All,
I ran into troubles when tried to calculate the NMR chemical shift. I used
sodium chloride (NaCl) as a test. The scf finished nicely (in parallel mode),
but when I did "x_nmr_lapw -p " (after "x_nmr_lapw -mode in1 -focus Na") I got
errors. The errors occur after the lapw2 run of the NMR calculation:
"EXECUTING: /home/n801/src/w2k/nmr -case nacl1 -mode current -green
-scratch /home/n801/scratch/ -noco "
The error message in "nmr.err.1" was:
"forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
nmr 000000000059F5C9 Unknown Unknown Unknown
nmr 000000000059DF40 Unknown Unknown Unknown
nmr 000000000054E7D2 Unknown Unknown Unknown
nmr 0000000000503AD8 Unknown Unknown Unknown
nmr 0000000000509D0B Unknown Unknown Unknown
libpthread.so.0 0000003EF3E0F710 Unknown Unknown Unknown
nmr 00000000004AB0F0 make_fopvec_green 281
make_fopvec_green_tmp_.F
nmr 000000000046E419 make_current_ 124
make_current_tmp_.F
nmr 000000000041608A MAIN__ 28 nmr.f
nmr 0000000000403AD6 Unknown Unknown Unknown
libc.so.6 0000003EF3A1ED1D Unknown Unknown Unknown
nmr 00000000004039C9 Unknown Unknown Unknown"
My configurations:
WIEN2k_13.1 (Release 17/6/2013)
ifort version 14.0.1
composer_xe_2013_sp1.1.106/mkl
CentOS release 6.4
Intel(R) Xeon(R) CPU E5-2667 v2 @ 3.30GHz
I also attached the stdout messages of the NMR runs.
Your help is very much appreciated.
Regards
SC Chung
$ x_nmr_lapw -mode in1 -focus Na
EXECUTING: /home/chung/src/w2k/nmr -case nacl1 -mode in1 -nodes 5 -green
-ovlpmax 0.6 -focus Na
:WARNINIG ATOM= 1 L= 0 HIGH OVERLAP between radial functions 0.84 setting
new lo energy: 0.30
:WARNINIG ATOM= 1 L= 0 HIGH OVERLAP between radial functions 0.72 setting
new lo energy: 0.80
:WARNINIG ATOM= 1 L= 0 HIGH OVERLAP between radial functions 0.61 setting
new lo energy: 1.30
NUMBER OF RADIAL FUNCTIONS IN case.in1_nmr
ATOM L=0 L=1 L=2 L=3
1 3 2 2
2 7 7 6
stop
klist .... ready
nmr: klists .... done
cd ./nmr_q0 ... x lapw1 -nmr -p -scratch /home/chung/scratch/
starting parallel lapw1 at Mon Aug 11 14:31:58 JST 2014
-> starting parallel LAPW1 jobs at Mon Aug 11 14:31:58 JST 2014
running LAPW1 in parallel mode (using .machines)
1 number_of_parallel_jobs
bash: -c: line 0: syntax error near unexpected token `makescratch_lapw'
bash: -c: line 0: `if ( ! -e /home/chung/scratch/ ) makescratch_lapw
/home/chung/scratch/'
[1] 18735
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
real 0m1.366s
user 0m19.086s
sys 0m2.121s
[1] + Done ( $remote $remotemachine "cd $PWD;$t
$ttt;rm -f .lock_$lockfile[$p]" ) >> .time1_$loop
fayalite01 fayalite01 fayalite01 fayalite01 fayalite01 fayalite01
fayalite01 fayalite01 fayalite01 fayalite01 fayalite01 fayalite01 fayalite01
fayalite01 fayalite01 fayalite01(47) Summary of lapw1para:
fayalite01 k=0 user=0 wallclock=0
0.095u 0.172s 0:03.40 7.6% 0+0k 0+232io 0pf+0w
cd ./nmr_pqx ... x lapw1 -nmr -p -scratch /home/chung/scratch/
starting parallel lapw1 at Mon Aug 11 14:32:01 JST 2014
-> starting parallel LAPW1 jobs at Mon Aug 11 14:32:01 JST 2014
running LAPW1 in parallel mode (using .machines)
1 number_of_parallel_jobs
bash: -c: line 0: syntax error near unexpected token `makescratch_lapw'
bash: -c: line 0: `if ( ! -e /home/chung/scratch/ ) makescratch_lapw
/home/chung/scratch/'
[1] 19030
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
real 0m1.368s
user 0m19.188s
sys 0m2.041s
[1] + Done ( $remote $remotemachine "cd $PWD;$t
$ttt;rm -f .lock_$lockfile[$p]" ) >> .time1_$loop
fayalite01 fayalite01 fayalite01 fayalite01 fayalite01 fayalite01
fayalite01 fayalite01 fayalite01 fayalite01 fayalite01 fayalite01 fayalite01
fayalite01 fayalite01 fayalite01(47) Summary of lapw1para:
fayalite01 k=0 user=0 wallclock=0
0.081u 0.184s 0:03.39 7.6% 0+0k 0+232io 0pf+0w
cd ./nmr_mqx ... x lapw1 -nmr -p -scratch /home/chung/scratch/
starting parallel lapw1 at Mon Aug 11 14:32:05 JST 2014
-> starting parallel LAPW1 jobs at Mon Aug 11 14:32:05 JST 2014
running LAPW1 in parallel mode (using .machines)
1 number_of_parallel_jobs
bash: -c: line 0: syntax error near unexpected token `makescratch_lapw'
bash: -c: line 0: `if ( ! -e /home/chung/scratch/ ) makescratch_lapw
/home/chung/scratch/'
[1] 19325
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
real 0m1.368s
user 0m19.254s
sys 0m2.001s
[1] + Done ( $remote $remotemachine "cd $PWD;$t
$ttt;rm -f .lock_$lockfile[$p]" ) >> .time1_$loop
fayalite01 fayalite01 fayalite01 fayalite01 fayalite01 fayalite01
fayalite01 fayalite01 fayalite01 fayalite01 fayalite01 fayalite01 fayalite01
fayalite01 fayalite01 fayalite01(47) Summary of lapw1para:
fayalite01 k=0 user=0 wallclock=0
0.090u 0.179s 0:03.39 7.6% 0+0k 0+232io 0pf+0w
cd ./nmr_pqy ... x lapw1 -nmr -p -scratch /home/chung/scratch/
starting parallel lapw1 at Mon Aug 11 14:32:08 JST 2014
-> starting parallel LAPW1 jobs at Mon Aug 11 14:32:08 JST 2014
running LAPW1 in parallel mode (using .machines)
1 number_of_parallel_jobs
bash: -c: line 0: syntax error near unexpected token `makescratch_lapw'
bash: -c: line 0: `if ( ! -e /home/chung/scratch/ ) makescratch_lapw
/home/chung/scratch/'
[1] 19621
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
real 0m1.384s
user 0m19.500s
sys 0m1.986s
[1] + Done ( $remote $remotemachine "cd $PWD;$t
$ttt;rm -f .lock_$lockfile[$p]" ) >> .time1_$loop
fayalite01 fayalite01 fayalite01 fayalite01 fayalite01 fayalite01
fayalite01 fayalite01 fayalite01 fayalite01 fayalite01 fayalite01 fayalite01
fayalite01 fayalite01 fayalite01(47) Summary of lapw1para:
fayalite01 k=0 user=0 wallclock=0
0.088u 0.184s 0:03.42 7.6% 0+0k 0+240io 0pf+0w
cd ./nmr_mqy ... x lapw1 -nmr -p -scratch /home/chung/scratch/
starting parallel lapw1 at Mon Aug 11 14:32:12 JST 2014
-> starting parallel LAPW1 jobs at Mon Aug 11 14:32:12 JST 2014
running LAPW1 in parallel mode (using .machines)
1 number_of_parallel_jobs
bash: -c: line 0: syntax error near unexpected token `makescratch_lapw'
bash: -c: line 0: `if ( ! -e /home/chung/scratch/ ) makescratch_lapw
/home/chung/scratch/'
[1] 19923
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
real 0m1.377s
user 0m19.254s
sys 0m2.004s
[1] + Done ( $remote $remotemachine "cd $PWD;$t
$ttt;rm -f .lock_$lockfile[$p]" ) >> .time1_$loop
fayalite01 fayalite01 fayalite01 fayalite01 fayalite01 fayalite01
fayalite01 fayalite01 fayalite01 fayalite01 fayalite01 fayalite01 fayalite01
fayalite01 fayalite01 fayalite01(47) Summary of lapw1para:
fayalite01 k=0 user=0 wallclock=0
0.100u 0.168s 0:03.40 7.6% 0+0k 0+232io 0pf+0w
cd ./nmr_pqz ... x lapw1 -nmr -p -scratch /home/chung/scratch/
starting parallel lapw1 at Mon Aug 11 14:32:15 JST 2014
-> starting parallel LAPW1 jobs at Mon Aug 11 14:32:15 JST 2014
running LAPW1 in parallel mode (using .machines)
1 number_of_parallel_jobs
bash: -c: line 0: syntax error near unexpected token `makescratch_lapw'
bash: -c: line 0: `if ( ! -e /home/chung/scratch/ ) makescratch_lapw
/home/chung/scratch/'
[1] 20220
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
real 0m1.362s
user 0m19.115s
sys 0m2.010s
[1] + Done ( $remote $remotemachine "cd $PWD;$t
$ttt;rm -f .lock_$lockfile[$p]" ) >> .time1_$loop
fayalite01 fayalite01 fayalite01 fayalite01 fayalite01 fayalite01
fayalite01 fayalite01 fayalite01 fayalite01 fayalite01 fayalite01 fayalite01
fayalite01 fayalite01 fayalite01(47) Summary of lapw1para:
fayalite01 k=0 user=0 wallclock=0
0.095u 0.169s 0:03.39 7.3% 0+0k 0+232io 0pf+0w
cd ./nmr_mqz ... x lapw1 -nmr -p -scratch /home/chung/scratch/
starting parallel lapw1 at Mon Aug 11 14:32:19 JST 2014
-> starting parallel LAPW1 jobs at Mon Aug 11 14:32:19 JST 2014
running LAPW1 in parallel mode (using .machines)
1 number_of_parallel_jobs
bash: -c: line 0: syntax error near unexpected token `makescratch_lapw'
bash: -c: line 0: `if ( ! -e /home/chung/scratch/ ) makescratch_lapw
/home/chung/scratch/'
[1] 20516
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
LAPW1 END
real 0m1.362s
user 0m19.132s
sys 0m2.038s
[1] + Done ( $remote $remotemachine "cd $PWD;$t
$ttt;rm -f .lock_$lockfile[$p]" ) >> .time1_$loop
fayalite01 fayalite01 fayalite01 fayalite01 fayalite01 fayalite01
fayalite01 fayalite01 fayalite01 fayalite01 fayalite01 fayalite01 fayalite01
fayalite01 fayalite01 fayalite01(47) Summary of lapw1para:
fayalite01 k=0 user=0 wallclock=0
0.090u 0.179s 0:03.39 7.6% 0+0k 0+232io 0pf+0w
lapw1 .... done
cd ./nmr_q0 ... x lapw2 -fermi -p -scratch /home/chung/scratch/
running LAPW2 in parallel mode
LAPW2 - FERMI; weighs written
FERMI only
0.067u 0.048s 0:00.12 83.3% 0+0k 0+912io 0pf+0w
cd ./nmr_pqx ... x lapw2 -fermi -p -scratch /home/chung/scratch/
running LAPW2 in parallel mode
LAPW2 - FERMI; weighs written
FERMI only
0.067u 0.050s 0:00.12 91.6% 0+0k 0+912io 0pf+0w
cd ./nmr_mqx ... x lapw2 -fermi -p -scratch /home/chung/scratch/
running LAPW2 in parallel mode
LAPW2 - FERMI; weighs written
FERMI only
0.068u 0.050s 0:00.12 91.6% 0+0k 0+912io 0pf+0w
cd ./nmr_pqy ... x lapw2 -fermi -p -scratch /home/chung/scratch/
running LAPW2 in parallel mode
LAPW2 - FERMI; weighs written
FERMI only
0.066u 0.050s 0:00.12 91.6% 0+0k 0+912io 0pf+0w
cd ./nmr_mqy ... x lapw2 -fermi -p -scratch /home/chung/scratch/
running LAPW2 in parallel mode
LAPW2 - FERMI; weighs written
FERMI only
0.069u 0.048s 0:00.12 83.3% 0+0k 0+912io 0pf+0w
cd ./nmr_pqz ... x lapw2 -fermi -p -scratch /home/chung/scratch/
running LAPW2 in parallel mode
LAPW2 - FERMI; weighs written
FERMI only
0.059u 0.047s 0:00.11 81.8% 0+0k 0+912io 0pf+0w
cd ./nmr_mqz ... x lapw2 -fermi -p -scratch /home/chung/scratch/
running LAPW2 in parallel mode
LAPW2 - FERMI; weighs written
FERMI only
0.070u 0.037s 0:00.11 90.9% 0+0k 0+912io 0pf+0w
weigh files .... ready
cd ./ ... x lcore -f nacl1
CORE END
0.011u 0.002s 0:00.01 100.0% 0+0k 0+744io 0pf+0w
cores .... ready
EXECUTING: /home/chung/src/w2k/nmr -case nacl1 -mode current -green
-scratch /home/chung/scratch/ -noco
[1] 21197
[1] Exit 174 ( ssh $machine[$p] "cd $dir; $exec -p
$loop" >> nmr.out.${loop} ) >& nmr.err.$loop
stop error
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